A modern advance in molecular visualization and animation

Industry leading software for 3D molecular visualization

Hundreds of thousands of scientists worldwide choose PyMOL to view, share, and analyze their molecular data.

In addition to being lightweight and fast, PyMOL creates images of peerless visualization quality, while offering the flexibility of Python-based development and scalability.


Bring your biochemistry to life

Produce publication quality images

  • Show important interactions, helpful representations, and key labels for any areas of interest
  • Produce stunning ray-traced images that add depth and shadowing to any structure
  • Create consistent figures that are easy to reproduce and modify

Simplify editing with scenes

  • Store snapshots of the current workspace to easily recall later
  • Use the thumbnails to easily distinguish between scenes
  • Add scenes to the timeline to create movies in only a few clicks

Create insightful movies with ease

  • Create movies that look stunning and convey the complexity of 3D systems
  • Use the new Timeline to create basic movies in a few clicks or devel deeper to unlock its full potential

What’s new in the PyMOL 3 interface?

Top Toolbar

The new top toolbar provides easy access to some common actions such as changing the selection mode, reorienting the camera, and launching various panels.

Scenes Panel

The new scenes panel allows the user to quickly store a snapshot of the workspace. These scenes can be easily recalled and now feature convenient thumbnails that can be recognized at a glance.

Contents Panel

The redesigned contents panel displays all objects and selections that are currently loaded into PyMOL. The ASHLC buttons allow the user to perform various actions including showing/hiding representations, applying specific colors, finding interactions, and much more.


The new timeline line is used to interpolate between values, show changes over time, and create insightful movies that breathe life into otherwise static systems. Simple movies can be created by adding scenes to the main camera track.

Communicate your science through images and videos

Micelle formation

Carbon nannotube

Cas9 inhibition in Scenes panel

Docking pose

DNA with transparent surface

Creating a simple movie in PyMOL 3

p38 binding

Aspirin binding site

APBS electrostatics GUI

Flagellar motor-hook complex from Salmonella

Aspirin animated

Bring your biochemistry to life

Training & Resources

Online certification courses

Learn how to unlock the power of movie making in PyMOL with our Visualizing Science with PyMOL 3 Online Certification Course.

PyMOL Wiki

Community-run support site that provides detailed pages on various features and commands. Additional resources and examples can be found in the “Quick Links” section.